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Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes
Open accessAbstract
BACKGROUND: Peptidoglycan is hydrolyzed by a diverse set of enzymes during bacterial growth, development and cell division. The N1pC/P60 proteins define a family of cell-wall peptidases that are widely represented in various bacterial lineages. Currently characterized members are known to hydrolyze D-gamma-glutamyl-meso-diaminopimelate or N-acetylmuramate-L-alanine linkages. RESULTS: Detailed analysis of the N1pC/P60 peptidases showed that these proteins define a large superfamily encompassing several diverse groups of proteins. In addition to the well characterized P60-like proteins, this superfamily includes the AcmB/LytN and YaeF/YiiX families of bacterial proteins, the amidase domain of bacterial and kinetoplastid glutathionylspermidine synthases (GSPSs), and several proteins from eukaryotes, phages, poxviruses, positive-strand RNA viruses, and certain archaea. The eukaryotic members include lecithin retinol acyltransferase (LRAT), nematode developmental regulator Egl-26, and candidate tumor suppressor H-rev107. These eukaryotic proteins, along with the bacterial YaeF/poxviral G6R family, show a circular permutation of the catalytic domain. We identified three conserved residues, namely a cysteine, a histidine and a polar residue, that are involved in the catalytic activities of this superfamily. Evolutionary analysis of this superfamily shows that it comprises four major families, with diverse domain architectures in each of them. CONCLUSIONS: Several related, but distinct, catalytic activities, such as murein degradation, acyl transfer and amide hydrolysis, have emerged in the N1pC/P60 superfamily. The three conserved catalytic residues of this superfamily are shown to be equivalent to the catalytic triad of the papain-like thiol peptidases. The predicted structural features indicate that the N1pC/P60 enzymes contain a fold similar to the papain-like peptidases, transglutaminases and arylamine acetyltransferases.
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“On the basis of its amino acid sequence and predicted tertiary structure, LRAT is classified as a member of the NlpC/P60 thiol peptidase protein superfamily (Figure 22).409”
From Chemistry of the Retinoid (Visual) Cycle (2014) · cites this paper as [409]
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“Despite being evolutionary ‘young’, LRAT belongs to an ancient and diverse group of proteins called N1pC/P60 [107].”
From Molecular Basis for Vitamin A Uptake and Storage in Vertebrates (2016) · cites this paper as [107]
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Metadata
- Authors
- Anantharaman, V., & Aravind, L.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Aravind, L
- Venue
- Genome Biology
- Published
- 2003-02-03
- Volume
- 4
- Issue
- 2
- Pages
- R11-R11
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC151301
- OpenAlex
- W2113183492
- Cited by
- 365
- References
- 73
- Citations by year
- 2026: 9 · 2025: 13 · 2024: 16 · 2023: 13 · 2022: 18 · 2021: 12 · 2020: 21 · 2019: 12 · 2018: 11 · 2017: 9 · 2016: 15 · 2015: 23 · 2014: 17 · 2013: 20 · 2012: 31
- FWCI
- 7.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- peptidoglycan hydrolase, circular permutation, conserved catalytic residues, catalytic triad, acyl transfer, amide hydrolysis, LRAT, domain architecture
- MeSH terms
- Amino Acid Sequence, Bacterial Proteins, Multigene Family, Models, Molecular, Molecular Sequence Data, Peptide Hydrolases, Phylogeny, Sequence Alignment, Sequence Homology, Amino Acid, Evolution, Molecular
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